Single-cell gene regulatory networks characterize colonic stem and immune cell homeostasis in Nr4a1 knockout mice

Recent findings suggest that the orphan nuclear receptor 4A (NR4A) can regulate cellular energetics and epithelial defenses, contributing to a resilient, disease-resistant phenotype. To further examine the effects of NR4A on intestinal epithelial, stromal, and immune cell homeostasis, we performed single-cell transcriptomics and differential gene network analysis in wild-type and whole-body Nr4a1 knockout mice. Here we observed a widespread effect of Nr4a1 deletion on intercellular communication involving intestinal stem cells, macrophages, T and B cells, and fibroblasts, indicating a complex and pervasive remodeling of the colonic epithelial and immune microenvironments and their regulatory networks. This alteration in cell-cell crosstalk was associated with an elevated single-cell entropy and colonic crypt-derived organoid growth, indicative of higher differentiation potential and stem-like properties in epithelial cells. Our work demonstrates that Nr4a1 serves as a critical regulatory factor in stem cell and immune homeostasis in the colon.